Customer Reviews

Biological Thermodynamics

5 star:		(4)
4 star:		(6)
3 star:		(0)
2 star:		(0)
1 star:		(3)

 

 

I teach a course in thermodynamics for college students in biology, as such, I thought the book could be useful, perhaps the new textbook for my course.
Possitive things:
* you will find real thermodynamics, biology and also historical notes in the book.
* there are not too many books that blend biology and thermodynamics in forms acceptable to biologist and physicists, this one does.
* it has an interesting selection of subjects

Problems:
* most of the time it has TOO many words, for those that like concise presentations, it is a problem. There are no evident forms to distinguish essential from accesory
* there is a bias towards bio-chemistry that introduces some additional difficulties for people with other backgrounds

My recommendation to the students
Main text: Kondepudi and Prigogine. Modern Thermodynamics
(extremely clear, concise and with historical notes but little biology)
Second text: Biological Thermodynamics by Haynie

I'm a Ph.D. student in computational modeling specializing in applications in physics and bioinformatics. My bachelor's degree is in biophysics. I have read numerous biosciences books and texbooks by leading authors. In my opinion this book is one of the best biophysics books I have ever read. I found this book accessible, which is important for students, and yet engaging. The author provides broad coverage of the subject and thoroughly explains basic concepts. For instance, the first law is covered in its own chapter, as is the second law. There are two chapters of Gibbs free energy, with many practical applications, and one on statistical thermodynamics. The chapter on kinetics is an appropriate complement to a book whose main subject is thermodynamics. The final chapter reads like a popular book, introducing students to a number of very interesting and exciting areas for research. This is truly a unique textbook. My guess is that this book might become a classic.

Forefront of its field
This review refers to the second edition. Professor Haynie brings to Biological Thermodynamics unusual literary flair and insight with demonstrated technical expertise in physics and biology. The book is a pleasure to read. I wondered whether the first edition could succeed as anything other than a monograph, or a supplementary text at best, but now a second edition is available. When I Googled the book I learned that it has been adopted for study in mechanical engineering courses in the University of California system and for biochemistry courses in Germany and Sweden. It is also cited in an economics paper in the peer-reviewed literature. The authors of that paper may have appreciated Professor Haynie's adaption of Richard Feynman's comments on the first law of thermodynamics: instead of Dennis the Menace playing with toy blocks of energy, we have a store clerk working with pennies of energy.
I think it is fair to say that Biological Thermodynamics has helped to create a new area of emphasis in undergraduate study, one that complements the work of the Gibbs Society in biophysics research. The interdisciplinary nature of Biological Thermodynamics is very much what is needed today at the undergraduate level: a deep sense of the relatedness of formerly distinct fields in science and engineering, and many examples of how the thinking in one traditional degree program influences, informs and inspires the thinking in another. Professor Haynie is not a recognized expert in the origin of life. Nevertheless, his book raises a number of provocative questions on the subject, and he provides students with the fundamental concepts and skills needed to appreciate and evaluate different hypotheses. His book is remarkably up-to-date, with numerous examples drawn from the primary literature of the past few years, and many references and recommendations for further reading. I am delighted to recommend this book as a text for students and a refresher for professors.

For neophytes to this field, like me, a more descriptive title for this book would be some jaw-breaker like "Thermal Physical Biochemistry". I'd picked the book up because I was interested in, e.g., the thermodynamic aspects of plant and animal physiology and morphology -- such as the shapes of leaves, snouts, beehives, etc. You won't find any of those subjects here, nor even any discussion of the thermodynamic differences between warm-blooded and cold-blooded animals other than a reference in a problem set. The book's scope is not really biology, but rather biochemistry. (According to an email I received from the author after posting an earlier version of this review, there is a professional society for "biological thermodynamics" that indeed focuses primarily on biochemistry. But if, like me, you're not a pro, you might be surprised to learn that the title phrase has such a narrow meaning. The author also tells me that there isn't enough material for a book about leaves, snouts, etc. at the undergraduate level; nonetheless, if that's what you're interested in, you should know it's not here.)

On the plus side, the book does have some down to earth explanations of concepts like entropy and free energy. It's also good at explaining why, for example, sometimes you want to use enthalpy and other times free energy. Most thermo textbooks just rattle off various combinations of variables, state functions and partial derviative relationships, without giving you any practical feel for when you'd use one or the other. In keeping with its emphasis on clarifying basic concepts, this book avoids calculus, and actually is better for it in many places.

That said, its approach is not purely thermodynamic. Thermo is based on macroscopic phenomena, even when discussing concepts like entropy. But this book's discussion of entropy is based on the statistical mechanics point of view from the get-go (even though stat mech isn't formally introduced until much later). It is not historically correct to say that "The Second Law is about the tendency of *particles* [emphasis in the original] to go from being concentrated to being spread out in space" (@60); the particle-based conception of the law followed the the law's discovery by several decades. The author's focus on particles fits in with the book's interest in chemistry. But the macroscopic point of view can give you many insights, too. (See, e.g., DeHoff's "Thermodynamics in Materials Science" for a non-biological example; ditto, in fact, for most engineering textbooks that deal with thermo.)

The book doesn't have any self-contained hints or solutions to any of the exercises. (The author tells me that those interested in solutions should write to him or the publisher for a solution set. I appreciate this, and I hope that news benefits you if you read the book; but in future editions this would be more helpful if stated on a website or in a preface.) There are also rather more typos, awkward phrases and awkward analogies than one would like to see in a 2nd edition. E.g., @73 the description of protein denaturation mixes up "decreases" with "increases"; there are too many negative signs in Table 4.1; a reaction is described as "cooperative" @ 97, even though this term is never defined in the text, leaving one to be mystifed by the glossary entry for "cooperativity" ("the degree of 'concertedness' of a change in conformation or arrangement of particles in a system," @402). (The author tells me that he will try to correct some of these problems in the next printing.) An explantion of the First Law analogizing energy to money is kind of OK in the limited context (@6), but the analogy is generally misleading, since money is not a conserved quantity even in economics theory. The author also has a tiresome and fitful quirk of mentioning the occupations of the fathers of many, though not all, of the scientists he names in the text.

Maybe the 3rd edition of this book will become a classic, but this edition isn't quite there yet.

If it is difficult to write a good and intelligible textbook on thermodynamics, it is next to impossible to write one that is not only good and intelligible, but also entertaining. Donald Haynie's book doesn't quite achieve that, but he makes a valiant effort, with numerous boxes to provide biological illustrations of the principles he is discussing. The first of these is called "hot viviparous lizard sex", and this gives a good indication of what is to follow in the others. The chapters become longer and more biological as the book proceeds, but the boxes become less frequent. This is a pity, because it is in the later chapters, when one sees the application of thermodynamics to biochemistry, that students will appreciate some light relief, and I doubt whether a footnote about Yesterday and Paul McCartney's knighthood will be enough to convince students of the importance of the Michaelis-Menten equation. At least one opportunity has been missed: the relevance of osmosis to everyday life is discussed in relation to the lysing of red blood cells if blood is diluted with water, but there is no mention of cooking. Proper treatment of blood in hospitals is, of course, very important, but it is hardly a matter of everyday experience for people who don't work in hospitals; on the other hand, it can be a valuable learning exercise to analyse the effect of adding a little salt when boiling carrots, even though virtually none of the salt (far too little to taste) remains when the water is discarded.

At times, one sees evidence of a failure to think things through. After telling us that Japanese honeybees can kill a hornet by forming a compact ball around it and raising its temperature by more than 10°C, the books asks "what if humans could somehow turn up their temperature at will?", forgetting that we were told (correctly) earlier on that whereas bumblebees can generate heat metabolically, honeybees cannot, so they use vigorous exercise and crowding, the same methods that work perfectly well (albeit not by 10°C) for humans.

There is little to criticize in the first half of the book, as the author clearly has a thorough understanding of chemical thermodynamics and a gift for presenting it in a way that is far more accessible than one finds in almost any other textbook on the subject. The main thing that I didn't like is that he wasn't able to decide whether to express energies in kJ, kcal or cal, switching arbitrarily between the three through the whole book. I haven't seen the first edition, but my guess is that the inconsistency is the result of a rather late and incompletely implemented decision to change from one system to another. So far as the problems are concerned (many thought-provoking problems at the end of every chapter), this may be a good thing, as readers of the biochemical literature need to be capable of understanding information presented in different symbols, terms and units from those they prefer. For the text, however, I can see no justification for it.

Although the more biological part of the book is in general correct and well written, there are some very unfortunate faults. The van 't Hoff plot is illustrated with a graph in which the zero on the abscissa is not labelled as such (the ordinate zero also, but that has no importance as it has no fundamental meaning). This is serious, because in the overwhelming majority of published van 't Hoff (and Arrhenius) plots, the zero is very far to the left of what is drawn, and one must not assume that the point where the axes cross is the origin. In the example given, the lowest abscissa value is, however, intended to represent zero, because the ordinate intercept is labelled as DeltaS0/R. This means that the "experimental" points span a more than 15-fold range of absolute temperature, so if the highest temperature used was 40°C, the lowest was about -250°C: this doesn't seem very plausible for an experiment of biological relevance, but if we assume that the lowest temperature was 0°C the highest was more than 4000°C, which seems even less credible. Why does it matter? It matters because estimation of entropy from a van 't Hoff or Arrhenius plot involves extrapolation of typically more than ten times the range of observations and thus results in a estimate with such a large statistical uncertainty that it is completely meaningless. Failure to understand this has resulted in a whole industry of nonsensical papers about entropy-enthalpy compensation. This is not to say that entropy-enthalpy compensation can never be a meaningful property, only that the entropy needs to be measured in a meaningful way. The idea of compensation appears later in the book, but without a clear indication that the thermodynamic parameters must come from calorimetric measurements, not from van 't Hoff plots.

Later in the same chapter, we read that "glucose phosphorylation is coupled to ATP hydrolysis", but that is again nonsense, because no hydrolysis is involved in glucose phosphorylation. It is true that the difference between standard Gibbs energies of ATP hydrolysis and glucose 6-phosphate hydrolysis tells us about the standard Gibbs energy of glucose phosphorylation, but that is as far as it goes; we can say nothing useful about the ratio of Gibbs energies. Haynie doesn't quite commit this sin, but he skates on thin ice when he talks about "efficiency" without being totally clear about what he means. Later on, we realize that the revolution in our understanding of metabolic control has passed him by, as he states that phosphofructokinase controls glycolysis, without any hints about why that might be a misleading statement. In the same context, he presents the DeltaG for the combination of aldolase and triose phosphate isomerase reactions in terms of ln([GAP]^2/[FBP]) without any mention of the implications of writing the logarithm of a concentration: what does it mean, and how can we make it acceptable? This would have been a good opportunity to remind the reader of the idea of a standard state, defined in the preceding chapter, but without any convincing explanation of why it is needed.

There is another missed opportunity in the next chapter, when the tired old cliché about being able to fit an elephant if you include enough parameters in your model is used to introduce the (perfectly valid) point that one should be cautious about adding parameters in a thoughtless way, followed by a comment that "entire books have been written on data analysis". True, but surely space could have been spared (in a chapter entitled "statistical thermodynamics") to mention that classical statistics developed to handle exactly this problem, and that that's what statistical tests are all about. The book returns to data analysis, but in an equally superficial and unhelpful way, in the later discussions of binding and kinetic data.

In discussing the Hill coefficient (symbolized as n), the book makes the usual error of relating the Hill equation to a model with n molecules of ligand binding simultaneously (despite the fact that Hill made it perfectly clear, a century ago, that that was not the right model), and then says that "n can in principle take any real value", providing only a half-hearted explanation of what non-integral values might mean. The confusion is compounded by equating negative cooperativity (n less than 1) with negative Hill coefficients (n less than 0). Negative Hill coefficients are possible, of course, in kinetic experiments, but not in binding experiments, the context in which the statement occurs. Another grotesque error occurs a few pages later, when the asymptotes of a curved Scatchard plot are drawn as if the straight parts of the curve lie along them; this error is responsible in the literature for some huge errors in estimates of binding constants.

In summary, there is much to like in this book, and as an introduction to chemical thermodynamics, it is excellent and readable, but for the more biological aspects it is more problematic, and I'd be reluctant to recommend it to students without some caveats. Nonetheless, a biochemistry student who read it and studied it thoroughly would certainly finish with a far better understanding of thermodynamics than is usual.

Dear friends,
the basic problem with this author(and hence the book) is, it preaches a lot of theory on thermodynamics which we hardly undestand just by reading.... he gives lot of review questions and problems at the end of chapters... Heartening... so far so good... And to your utter disappointment NO ANSWERS for the problems...an author of Mr Haynies' eminence should understand a little bit of student psychology... such a complicated subject like thermodynamics has to be taught through illustrative problems(a problem with detailed solution after explaining a theoretical aspect) which is totally absent in the book. In the preface (page xiii)author boasts that he has kept some 'open ended questions" which donot have a definite answer and he claims that it is the strength of this book!!!! phew!!!!!!!!!!! If you think that it is a strength , then you should gives us the different possible answers and justify your stand. Here there is nothing!!!!!!! NO ANSWERS... only questions... This book is uselesss,,,,, teethless... Don't buy this book

As someone who has used the book during his graduate studies in biophysical chemistry (the field of biopolymer conformational dynamics), I warmly recomend this book to any student/researcher interested in learning more about this field. The book offers a solid foundation to those interested in exploring the field in greater details.

For people with little insight (but interest) in thermodynamics this book is mandatory. For me personally it has been a quick way to freshen up the concepts of thermodynamics. The book is in large parts well written with many easy to understand examples of otherwise diffucult topics.

This book is cleverly written. What comes through on every page is Dr. Haynie's breadth of knowledge and enthusiasm for his subject. Dr. Haynie proved that a good scientific text need not be boring. Students who want to learn how thermodynamics relates to everyday life and how their body works will love this book.

I am doing this review from the 2001 (1st edition) that I read in 2005; but from a skim of the new edition via the Amazon reader, however, it looks like some of the same errors exist. The book, overall is a decent read, but it should be titled "biochemical thermodynamics", the thermodynamics of biochemical operations (most of the book is structured around the thermodynamics of protein folding, the author's PhD thesis). Biological thermodynamics, correctly, would be the predator-prey type of energetic/thermodynamic interactions outlined by Austrian-born American physical chemist Alfred Lotka in 1922 and 1924.

The main reason that I posted this review is that the etymology of the word thermodynamics is off by twelve years. On page 26 (22 of first edition), Haynie states "energy has been around for, well, since the `beginning', but the word thermodynamics was not coined until 1840, from the Greek roots therme, heat, and dynamis, power."

Correctly, the conjunction "thermo-dynamic" was used in 1849 by Scottish physicist William Thomson (referring to a perfect thermodynamic engine, on the etymology of `perfect' vacuum, of the Otto von Guericke type (1647) in relation to a Sadi Carnot type reversible engine (1824). The word "thermodynamics" was coined by Thomson in 1854 as: "Thermo-dynamics: the subjects [of] the relation of heat to forces acting between contiguous parts of bodies, and the relation of heat to electrical agency."

In addition, the term energy has not been around "since the beginning". The original etymology of the term "energy" stems from the works of Greek philosopher Aristotle, particularly his c. 350 Metaphysics, who used the term enérgeia to mean act or `activity', `actuality'; whereas the modern physics etymology of the term "energy" stems from the 1807 lectures of English physicist and physician Thomas Young who used the term energy in place of the older term vis viva, in the sense of kinetic energy.

The subject of thermodynamics wasn't even in existence in 1840. This leads one to question Haynie's underlying knowledge of the subject?